About ClarID-Tools
ClarID-Tools is developed at CNAG, Barcelona, Spain, as the reference command-line implementation of the ClarID identifier approach.
Scope
Subject and biosample IDs
Encoding and decoding for the two ClarID entity types currently implemented by the toolkit.
Controlled vocabularies
YAML codebook support for labels, aliases, compact stubs, and project-specific vocabulary choices.
Schema-backed checks
JSON Schema validation for codebook structure before identifiers are generated or decoded.
Operational workflows
Reproducible command-line examples, QR-code workflows, and GDC-derived use cases.
In short: the paper defines the concept; this repository shows how to run it.
Relationship to the Paper
The paper describes the motivation, identifier design, and intended use in biomedical metadata integration. This documentation describes the operational implementation for the current software release.
This includes the exact CLI behavior, the codebook configuration model, practical encode/decode workflows, reproducible examples, and QR-code generation.
If wording in the paper and implementation documentation ever diverge, the paper should be treated as the conceptual description and this documentation as the operational guide for the current software release.
Developers
Acknowledgments
ClarID-Tools was developed with support from Ivo G. Gut and the Genome Research Unit Biomedical Genomics Group at CNAG.